SAMBA: hardware accelerator for biological sequence comparison.
BACKGROUND
SAMBA (Systolic Accelerator for Molecular Biological Applications) is a 128 processor hardware accelerator for speeding up the sequence comparison process. The short-term objective is to provide a low-cost board to boost PC or workstation performance on this class of applications. This paper places SAMBA amongst other existing systems and highlights the original features.


RESULTS
Real performance obtained from the prototype is demonstrated. For example, a sequence of 300 amino acids is scanned against SWISS-PROT-34 (21 210 389 residues) in 30 s using the Smith and Waterman algorithm. More time-consuming applications, like the bank-to-bank comparison, are computed in a few hours instead of days on standard workstations. Technology allows the prototype to fit onto a single PCI board for plugging into any PC or workstation.


BACKGROUND
SAMBA can be tested on the WEB server at URL http://www.irisa.fr/SAMBA/.
Guerdoux-Jamet
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IRISA, Rennes, France. lavenier@irisa.fr
Lavenier
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D000465:Algorithms; D019295:Computational Biology / Q000639:trends; D003201:Computers / Q000639:trends; D003205:Computing Methodologies; D016208:Databases, Factual; D016678:Genome; D005810:Multigene Family / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment / Q000295:instrumentation / Q000379:methods / Q000639:trends; D017421:Sequence Analysis / Q000295:instrumentation* / Q000379:methods* / Q000639:trends